Keyboard shortcuts!
A lot of the JavaScript UI widgets that are a replacement for native/browser controls _look_ nicer, but that doesn't mean the overall UX is better. Keyboard shortcuts, auto-focus, etc. are crucial for things like alert/confirm/prompt.
For completeness, would be nice to see matching confirm/prompt as well.
And I agree - there should be an option for clobbering/overriding the original alert function.